Rain and Rooftops
by midnight-tiptoes
Summary: When Molly Hooper told Sherlock Holmes he'd always have her, she never knew it would lead to this. Sherlock takes Molly on the run with him. Much to his dismay
1. Chapter 1

**Rain and Rooftops**

_Summary:When Molly Hooper told Sherlock Holmes he'd always have her, she never knew it would lead to this. Sherlock takes Molly on the run with him. Much to his dismay_

_Chapter One_  
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She stood under the umbrella, trying not to let the cold affect her as much as it did. She looks up at him but didn't say anything, instead leaving him to his thoughts. Molly knew this wasn't the position that he had wanted either of them, exceptionally him, to be in but here they are and they must move forward.

She felt the strong urge to continually apologize although, to be frank, it really wasn't her fault that they were in the predicament that they were in. Yet she could read him, much to his chagrin, and she knew he would rather have anyone here, even his land lady seemed more appealing than she did. All things considering she knew that she wasn't fully to blame here.

"Molly lets getting going. I don't think we're going to find anything here." his deep voice brought her out of her reverie and back to the night street as the rain fell down upon them. He starts walking ahead of her, not giving her a even a moments glance. Molly always wondered what it would be like to spend an evening with Sherlock in Paris yet this certainly didn't live up to her exceptions.

"Alrighty," She says almost to herself and follows quickly behind him as he hails a cab that would take them to the small motel they had been staying at for the past week or two. Sherlock didn't really open up to her about the cases that he seemed to be working on, but what little information he did let her in on, she was able to piece together a bit of the puzzle

It seemed he was trying to take down a very large and very dangerous crime circle that spread almost the whole of Europe and from what she gathered Jim Moriarty seemed to be at the center of it all. Or used to be, now that his death at the rooftop of Bart's put him out of commission. A second in command seemed to have taken over duties of wreaking havoc on the world.

A man whom Sherlock simply referred to as Moran.

In the comfort of the dry cab, she tucked her slick umbrella under her legs on the floor and turned her gaze onto Sherlock. He was deep in thought, his expression conveying nothing but boredom, but his eyes were blinking at a quicker pace than normal, a tell-tale sign that his brain was working in high gear. They had been left standing in the rain for almost an hour waiting for something...anything to happen. She wasn't exactly sure what he had up his sleeve but he wasn't entirely forthcoming about his plans either.

It had been a whole two weeks since she had been forced to join him in Paris and she's not exactly sure she wants to be the only person he can turn to anymore. Before, she looked to Sherlock and saw this glamorous, excitingly devilish man she only wished would notice her. He really did epitomize everything mothers warned their daughters from. While he was devastatingly handsome and was undoubtedly the cleverest person she's ever met, he was also rude. And destructive. He didn't know how to sit still and have a normal life. Not a very reliable person either, to say the least.

The past fourteen days, give or take, and taken an emotional, and physical, toll on the tiny former pathologist. Her life was turned upside down and all because she had decided to put all of her blind faith in a man who couldn't even remember simple things from primary school.

- ! - ! - ! - ! - ! - ! -

_One month earlier_

Swinging her large stripped bag over her shoulder, Molly Hooper makes her way out of St. Bartholomew's Hospital in central London and started her trek home for the first time in almost two days. Still in the same clothes she had picked out hours previous, her whole body felt weighed down. Even her bones felts like cement. The whole city seemed ablaze with nothing but the death off Sherlock Holmes, the great (fake) detective. Reporters stood outside of the building for hours afterwards, trying to get glimpse of where he had fallen, to get interviews with anyone who he seemed close with. She seemed to fade into the background.

"Excuse me, Miss?" a deep voice from behind Molly catches her attention and forces her to stop. Whipping her head around, she sees a tall, stocky man in a suit striding towards her. He had blonde, crew cut hair and a smile that didn't quite reach his eyes. Which she can see, even under the blanket of the late evening, is astonishingly blue. She cracked a tight smile and waited for him to approach her, really just wanting to cut and run. "Can I ask you a few questions?"

Ah. Another reporter. Although why he was bothering with her was rather curious. "Well, I don't really feel comfortable discussing the death of Mr. Holmes." she declines politely, not giving him the chance to even ask her anything at all.

This time his smile was genuine and he stopped short in front of her. He folded his hands in front of him and it surprised her that he didn't look surprised at all, like he had been expecting her rejection before even stopping her in the first place. That's the most probable reason for him to even try asking her questions at all, she concludes. Exhausted all his leads and now asking whoever was walking out the door. "I didn't even get to ask about Mr. Holmes." The cheeky reporter reminds her.

She returns his grin and told him he didn't even have to. What else could someone possibly want from her? "Besides, how'd you even know I worked here? I might have been a patient."

"Most patients don't wear St. Bartholomew name tags," he leaned in near her breast where her name badge was pressed and she felt her checks flush red. "Molly Hooper."

Taking a few steps back, slightly embarrassed, Molly offered him a weak laugh. "Yes, well, you already have my answer. I cannot, and will not, discuss this much further. Sorry." She silently reprimands herself for apologizing, a nervous habit she had developed from an early age.

He smiles a bit more widely and placed his hands behind his back now, puffing out his chest. "Well then, can you tell me one thing then, Miss. Hooper? Just answer me this: did you indeed know Mr. Holmes? Did you ever work with him and if so did you ever suspect him to be suicidal?"

Molly stared up at him for a second, trying to regain her composure, lying never came easily for her. "Well, that seems to be more than one question." She laughs weakly; stalling. "But no, I did not know Sh. . I mean.. Mr. Holmes very well. Not at all really. I mean. . .he just sort of-well you know, walked about the hospital as if he kinda owned it. I really only know him by reputation." She stumbles over her words and hopes that the darkness of night hides any of the blushes that had risen to her face. Again.

"Well then if you are so adamant about not offering the general public answers to the questions they deserve since they did indeed label him a hero, I shall let you go on your merry way." The reporter steps aside and gives her a small bow. "It was nice talking to you Molly."

The quick ending of their conversation left her both relieved and confused. She had never really dealt with reporters before but had always gotten the general consensus that they would go to any means to get coverage on a story. Or maybe she just let the media and their portrayal of it shadow her judgment. Either way, she stepped around him and said her goodbyes as well.

Molly could feel his eyes on her but she keep on walking because she wanted to get home and see if Sherlock was making out okay.

-! - ! - ! - ! - ! -

Making sure she looked halfway decent before returning to her flat, Molly walked in to find Sherlock sitting at her small dining room table reading an article on her laptop. She was a bit embarrassed by the fact that she hadn't bothered to have done the morning dishes or put away any of the old newspapers. She had never thought someone would be in her flat before she had the chance to clean up, let alone the man she fancied.

"Hello," she offers a timid greeting while setting her bag and coat on the floor beside her sofa and walking slowly towards him.

"Hello, Molly. How are things?" He asked, not bothering to look up from what he was reading. "Oh by the way I took a shower once I got here. Didn't want to let the blood in my hair dry any longer than necessary." he said as if it was the most natural thing in the world.

"Oh. Okay. That's fine. I kinda figured you would." She smiles; in all reality she had never thought he would have used her shower. The absurdity of their situation was leaving her with whiplash. Another horrifying thought enters her head. She hopes he wasn't weirded out by all the pink. Even she knew it was a bit much but she did enjoy looking at the friendly color.

"So I take it everything worked out?" he inquires, his attention finally turned from the screen to hers for a brief minute to let her know that he was listening and wanted to hear what she had to say.

"Oh yes. Everything I thought we might run into as possible problems never arose. The paperwork is all done and the John Doe that will be in you casket is set to go. Just need conformation about the funeral arrangements." She was twisting her fingers together, trying to keep herself focused.

This isn't a dream or some trick. This is her life, for the time being as it were, and if she doesn't focus on the good (that she's saved his life and three of his closest friends) her mind will get sucked into a place she isn't so keen on visiting right now. A place where she is reminded of all the hurt that is inevitably going to fall on those same people she considers friends as well.

"Excellent. You did great Molly." This time when he spoke, he looks her right in the eyes, like he meant what he had just said. She could feel her face growing hot and cursed her pale skin and the effects he had on her.

"I'll always be here for you Sherlock." She doesn't want to come off as needy, but she wanted him to fully understand that he always had her to turn to. She knew she didn't really matter as much as John or his Mrs. Hudson, but as long as he knew someone else was out there willing to help him, she was okay with that.

"Yes. Well, thank you Molly." He replies, clearing his throat uncomfortably. Standing, he unbuttons the blazer he had been wearing and tossed if over the back of the chair. "I won't be here long. Just until the funeral to make sure everything has worked out okay."

"Yes. Of course. No. Stay as long as you like." As she fumbles over her words again, her eyes quickly avert to the floor. Molly can feel his eyes on her and wanting to say something, anything, that doesn't make her sound like a complete moron, she offers to make him some tea or coffee.

"Just tea please." He turns away from her and walks to the window, looking out on the street down below. She watches his back for a second longer before making her way into the kitchen to make them both a much needed cup of tea.

- ! - ! - ! - ! - ! -

He walks into St. Bartholomew's hospital under the very minimal disguise of a white lab coat and a badge stolen from a sleeping medical student. In the wee hours of the morning it seems as if the prestigious hospital falsely assumed they were secure from intrusions of his kind.

He walked through the halls of the basement to the mortuary where he knew he was to find the body he was seeking. He keeps is head straight, not trying to draw any unwanted attention to him. It seems as if the whole floor had been deserted and he was the only man in the entire building. He prefers getting lost in a crowd, he thinks dismissively, the quietness only works at put him on edge.

He enters the room where they bodies are kept, keeping his head all the more bowed. The body of Sherlock Holmes lay somewhere in this room, all he had to do was find it. It appears to be as easy as stealing sweets from a child because the ease he discovers the slab in which his battered body is almost laughable.

Of course, when he pulls out the door he finds that it was not the body of Sherlock Holmes. Shutting the door, he checks to make sure he read the name right. Indeed, on the front it says Holmes, Sherlock. Had they moved the body? Had they placed his body in a different area? But why on earth would they do that? He painstakingly went through all the cadavers that they had here, ten in total for the day, and not one of them being Sherlock Holmes.

He steps back, trying to piece together a very strange puzzle. Before blowing his brains out Jim had instructed he was to make sure that Sherlock was to be, in fact, dead as a doornail. Instead all he found was a body surrounded by a group of doctors and pedestrians and he found it hard to really make sure if he had died and or not.

It was better to be safe than sorry. Jim Moriarty had a knack of getting bored and causing problems, or as he called it creating games, to keep him entertained. However, he was always the one who took a more low key type of style when operating. And right now it was important to make sure Sherlock Holmes had indeed died.

Turning to the computer, he hacked into their system with ease using the technique that had honed over the years. Bringing up the death certificate of one Mr. Sherlock Holmes he searched the database. He tsked over how simple this really was turning out to be.

He found what he was looking for, and seemed a bit confused by what he was reading. He was declared dead by none other than Pathologist Molly Hooper. The same Molly Hooper he had tried, unsuccessfully, to obtain information from earlier that evening. He stood rooted in that one spot trying to piece together what was going on.

No body. No Body. He kept telling himself that over and over again in his head. And yet he had been declared dead. And finally Sebastian Moran wondered if maybe that meek little Molly Hooper was somehow involved in a cover up.

- ! - ! - ! - ! - ! -

_Present day. Paris, France_

It was at times like these he wished he had a violin to play, to help sort out his thinking process. It was eerily quiet in their motel room and it was a great way to collect and process what he had dealt with today. Sherlock turned to look at Molly as she was curled up on the far side of her twin bed with a book lying on top of her body.

Was it remorse he was feeling for having involved her in this? He knew John would say it was and maybe he knew it was too. It was a feeling he wasn't too sure what to do with. He certainly felt ill at ease knowing he was the reason she almost lost her life just few short weeks ago. He had never wanted things to end up like this. Yet Sherlock knew he had to keep Molly safe and London was not safe. And keeping Molly safe would keep John, and Ms. Hudson and Lestrade all safe.

Funny, how life worked sometimes he thought. And he had to find a place to buy a violin.

- ! - ! - ! - ! - ! -


	2. Chapter 2

_**Rain and Rooftops / Chapter Two**_

_**Disclaimer / Don't own a thing.**_

Its a few days after his funeral and Molly can tell he's getting ready to leave soon. Not that he's given her any set date of when he'll be heading off for god knows where (like he says much to her anyways) but she can tell he's getting antsy. Some nights she'll come home to see him pacing throughout her living area, his brow furrowed deep in thought. She's given up on trying to start actual conversation with him now. Much like the scene she's just stumbled in to.

Setting her bag down on the small chair and shrugging out of her favorite comfy cardigan, she picks up the mail that had been tossed haphazardly across the table. Junk. Junk. Bill. Letter offering some amazing new deal she's missing out on. Bill. She sighed and tossed them back on the table. That seemed to snap Sherlock's attention towards her.

He looked surprised to see her. As if standing in the living room of her apartment was somehow mindboggling. "Didn't you hear a word I just said?" he asked her, irritation laced in his words.

"Sorry?"

"I asked you to head down to the drugstore and pick me up a few things. Did you get sidetracked on the way there and forget?"

She pursed her lips, trying to squelch the feeling of being his personal maid/secretary/landlady/general all around whipping girl, before she vaguely remembers a conversation she had overhead between John and Sherlock a few months prior. Sherlock was complaining to his agitated friend that John was ignoring him. To which John hotly retorted that "For someone who can spot anything, he's remarkably oblivious as to when he's talking to himself like a madman."

"I've no idea what you're talking about." She sighs and takes a seat on the couch Sherlock's called home for the past few nights. "I just got off work. Literally minutes ago. Maybe you _meant_ to tell me?" Molly suggests, trying not to let him feel too embarrassed about talking to himself as she was out. She doubted he ever would be, but it's always nice to make sure.

"How long were you gone?"

"About nine hours. Give or take."

He nods and turns his back towards her. The room grows quiet as Molly sees Toby perch himself on the computer desk in front of Sherlock. He detests the tiny feline which only makes him chase after the brooding man all the more. She almost chuckles at the irony of that.

"Well, now that you're here and listening," he sniffs, turning to give her a quick glance. "I hope. I do, in fact, need a few things from you before I leave tonight."

She's struck cold. "You're leaving…tonight?" she squeaks. Molly's not sure why she's so startled by his revelation. It's not as if she wasn't expecting it. It's just sudden, that's all.

"Yes. It's high time I left London. Funeral has passed and interest is starting to wane. At least for the public, anyways." His hands go behind his back and he strides towards her. She gazes up at his towering frame, a tiny bit overwhelmed. He always leaves her feeling like this. "I need you to procure small, various items for me. If it's not too much trouble."

She shakes her head, but he never expects her to say no to him.

"Good. First, I need a phone. Something cheap. Nothing traceable. New clothing. Large shirt. Button up, preferably. No. Not button up. Something simple, however. Pants, 34 waist, 32 length. You should probably be writing this down." He's talking quickly and the pacing is back, but it's not frantic movements like before. She's staring and her mouth is open before she grabs hold of her bearings and quickly grabs a pen to write on the back of junk mail.

"You know, you're probably going to need…"

She's cut off by him tossing a tiny box to her, catching her off guard. She clumsily drops it and she tries not to let her cheeks burn when she notices him roll his eyes. It's a small velvet box, one she's long to see someone like him give her. Opening it slowly, she sees beautiful diamond cuff links. Her head snaps up to look at him. "You want me to sell these? Did you steal them?"

"Yes. And these too." He tosses another tiny box her way, this time it lands near her on the couch, a deliberate miss. "And no I did not steal them." He sneers. Molly opens the box to see tie pins.

"It's not much right now, but it's enough to get me to where I need to go."

She wants to ask where that someplace might be but doesn't want to overstep her bounds. She just nods. When neither of them says anything, he obviously is dismissing her to fetch his required items.

When she turns several hours later, still surprised at how much she fetched the cufflinks for, she finds the living room completely empty. Every day, since he's been cooped up with her, Molly's always come home to find him in the living area. Or in the kitchen. But now he's nowhere in sight. Her stomach drops and a feeling of dread sweeps over her. He's sent her away so he can leave without having to say goodbye. What a selfish prick, she thinks bitterly. After all she's done –

"What on earth are you doing standing in the doorway like that?" his voice booms over her thoughts, startling her. She turns and almost drops her bags in utter disbelief. His usually long curly hair is gone, in its place much shorter hair. "What?"

"N-Nothing. It's just. I'm not used to seeing your hair so short."

"Ah, yes. Well, desperate times call for desperate measures. And don't worry, I cleaned up the mess. Did you get everything?"

Molly nods her head and turns to the bags she's carrying. Damn. He even looks amazing with his hair chopped off. Makes her want to run her hands through his hair all the more. Clearing her throat, she sets them down and shows him what she's brought. Two types of shirts: one soft cotton t-shirt and one sweater. Molly wasn't sure where he was going, or what the weather would bring, so she prepared for either situation. She debated on jeans or slacks but since she's almost positive she's never seen him in jeans, she chose them instead. Also hands him a small pre-paid smart phone that comes with internet if he wished. She knows he's attached to his phone and couldn't live without one.

He goes over everything and she hands him an envelope with the couple thousand pounds his never worn jewelry raised. He doesn't open it and turns to her. Molly finds herself staring at his hair because, really, it's such a nice change. His cheekbones are more prominent and his eyes take center stage; no longer hidden behind curls. Before she even realizes what is happening he has inched slowly towards her. It reminds her of that night in the lab, the one that changed her life irrevocably. His eyes are directly on hers and the gaze is so intense, she wants to look away.

"Thank you, Molly. You've done a great deal for me with nothing in return. I'll…forever be grateful." He's speaking softly and Molly feels like she can't breathe. It's not as if he hasn't been kind to her before, it's just such a rarity.

"Sherlock," she gulps, deciding on whether she wants to ask him this or not, but her gut out matches her brain and before she has time to think, words are tumbling out of her mouth. "Are you sure you want to do this? Jim is….Moriarty is dead. John is no longer in danger. Can't you at least.."

Any softness that was previously held in his voice was gone now. He takes a step back, his eyes hard now. "I wish it were that simple. You think he's the only one out there? That Moriarty is the only psychopath to exist? John's been kidnapped. Had a bomb strapped to his chest. A snipers gun trained on him. All because of his open association with me. Moriarty was a consulting criminal. He did bad things for high prices. Are you so sure he'd merely operate alone? He plants bomb in London for fun. Can bring the British and American governments to their knees. How simplistic do you have to be to entertain the notion that he'd do that all alone."

Molly feels her knees grow week and she's so utterly confused. It was a simple question, really. She had no idea where this…this came from. It's almost as if he's justifying it. Leaving John behind. Must be so hard for him, she muses. "So…you're looking for Ji…Moriarty's John Watson?"

"His what?"

"His John." She answers softly. "You've got John. Someone you trust more than anyone. Your…weakness." His brows furrow and she hastily adds "You're looking for someone that Jim trusted more than anything. His right hand."

Sherlock's back is stiff but the tiniest of smiles touches his face. "His right hand."

**-!-!-!-!-!-!-!-!-!-!-**

Watching the tiny brunette bounce away from her flat, Sebastian sat up in his car and gave it a few minutes before getting out and strolling into the three story brick building, telling Max to wait in the car. Since he'd discovered the news that there was no body for Sherlock Holmes, supposedly, he'd being watching Miss. Hooper and John Watson, alternating nights. Both painfully boring people.

Or mourning. He supposed that was an option as well.

Either way he'd already tried breaking into the now previous residence of Sherlock Holmes, only to find that John Watson never left the bloody flat. And the terribly fussing old bag was there whenever he decided to grace the world with his presence. So he'd begin tailing the tiny git. He only ever left the flat to go to see a psychiatrist.

Interesting.

He actually thought he'd been on to something. Until a quick break in here, a sneak peek at the files there only provided proof of a severely wounded man. Wounded by war and loss of numerous friends. Feeling alone with trust issues, he had a hard time opening up and blah blah blah. Based on these files, he'd think John Watson a weak man if he hadn't known better.

After a few seconds with the lock, he quickly pushes open the door and steps inside. A small grey cat eyes him suspiciously and Sebastian curls his lips. Horrible, sneaky creatures; like furry snakes. He begins looking around and is surprised at the tidiness of it. There are lots of books and magazines, but it's a structured chaos. He starts opening drawers to the desk and flipping through various papers and letters she has stored there.

Booting up the computer, he heads to the bedroom down the hall when he hears the door open. Standing still, afraid to move a muscle, Sebastian barely breathes. Lifting his body onto the balls of his feet; he waits for the unexpected visitor to make some sort of noise. He tiptoes quietly into the nearest open door, which happens to be the bathroom.

"Hiya, boy." A cheerful womanly voice her recognizes as Molly finally says. "Miss me?" she chuckles at her horribly bad joke and Sebastian rolls his eyes.

Why the fuck was she home? He'd remembered her work schedule by heart. She was working till nine tonight. It's not even bloody noon. And why the fuck didn't Max send him a warning text? He only brought the useless sod with him to keep a look out. Great fucking job he did.

"Hmm..I don't remember leaving that on." He barely hears her mutter.

Fuck.

Bring out his phone he quickly sends his moron partner a text_. She came home early. Do something to get rid of her._ It's as if he can feel things slipping out of his control because almost immediately he hears a bloodcurdling scream. Jerking his head up, he sees her standing in the doorway. Her eyes are as wide as saucers and they both stand there, staring each other down.

Fuck.

She scrambles backwards and runs toward the living room. He runs after her but she's started tossing things in his way. She's faster than he's given her credit for because before he knows it she's down the stairs. She's out the door and he's almost got her, he can literally reach out and grab her when a loud _POP_ rings in his ear.

Everything seems to go in slow motion as he looks down to see if he's been wounded. His first instinct is to get down and find cover. But this isn't a battlefield. This is a plan quickly spiraling out of his grasp. How the fuck did this get so bad so fast? He looks up and see's that it's the tiny woman who's been hit. She looks so frightened. So pale. He remembers James trying to seduce her to get closer to Sherlock. His prognosis of her was never favorable. Easily manipulated and very gullible, she cares too much. Like a tiny bird, he once laughed.

It's a few seconds since the gun shot rang out and in those precious moments where Sebastian lost his wits, the woman did not, however. She was already running down the street. He turns to the car and see's Max aiming the gun from the back of the car and he runs over, his whole body shaking with anger.

"What the fuck is wrong with you?"

"You told me to get rid of her."

"I also told you to keep a look out!" he was starting the car and pulling out of the neighborhood, just as people were starting to come and inspect the scene. "And you shot her? In broad daylight? While I was standing there? Are you mentally challenged or are you just that stupid?"

Sebastian's making sure not to speed, doesn't want to draw too much attention to the car. The dark haired man crawls back into the front space and, when he positions himself down, Sebastian punches him in the cheek, sending him back into the door. "I swear to Christ I didn't see her!" he's shouting now too. "I looked down at my phone for a few seconds. That's it! I swear I didn't see her!" he's quiet for a moment, rubbing his cheek. "I'm sorry." He mutters.

"Yeah. Me too."

**-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-**

She's running down the street as fast as her legs will carry her. Holding her arm, she feels the warm, thick liquid drip drip dripping down her side. Her whole mind is jumbled and she can only think of one place she can go.

**-!-!-!-!-!-!-!-!-!-!-!-!-!-!-!-**

**So there you have it, chapter two. I know this is a really crappy place to leave off but if I didn't post this now, I wouldn't have been able to get it up before work. I've already started on the next part and there are a lot of things that chapter answers. The next chapter won't be to terribly long, just wanted to get some things started and stated before Molly joins Sherlock on the run! I hope you like it!**


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